Antigen

Antigen Class

TFs and others

Antigen

HDAC3

Cell type

Cell type Class

Prostate

Cell type

LNCAP

Primary Tissue

Prostate

Tissue Diagnosis

Carcinoma

Sample

source_name

prostate tumor

cell line

LNCaP

treatment

pGIPZ

antibody

HDAC3, Abcam, ab7030, GR3202599-3

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Chromatin in nuclear fraction were sheared to 200-500bp using an Covaris M220 Focused-ultrasonicator, Lysates were clarified from sonicated nuclei and protein-DNA complexes were immunoprecipitated using the indicated antibody. DNA was then reverse crosslinked from protein and purified. ChIP-seq libraries were prepared from 3-5ng ChIPped DNA by using NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645S), according to the manufacturer's instructions. Postamplification libraries were size selected at 250–450 bp in length using Agencourt AMPure XP beads from Beckman Coulter and were quantified using the Library Quantification Kit from Illiumina (Kapa Biosystems, KK4603). Libraries were pooled to a final concentration of 10nM and sequenced single-end using the Illumina HiSeq 4000.

Sequencing Platform

instrument_model

Illumina HiScanSQ

hg38

Number of total reads

12027559

Reads aligned (%)

90.3

Duplicates removed (%)

22.3

Number of peaks

2258 (qval < 1E-05)

hg19

Number of total reads

12027559

Reads aligned (%)

89.6

Duplicates removed (%)

22.5

Number of peaks

2140 (qval < 1E-05)